Without spending a lot of time to read and digest everything in this thread, my first thought is have you considered using an ARM (or similar) CPU running a 6800 emulator, rather than trying to emulate it more precisely via an FPGA? I've had good success with reverse engineering old systems and emulating the old CPU/MCU on an ARM CPU, along with various other external devices, combined with new modern interfaces. For example, old systems that use lots of data/address lines to interfaces can be replaced with SPI/I2C. It generally requires disassembly of the hex file into assembly code, and then further analysis, either automated or manual, to generate some C or other higher level code, in order to fully understand everything, and then modify the code as necessary to utilize the modern interfaces. Not a trivial task at all, but for me so very rewarding when I totally reverse engineer a system like that.
Trying to do the same via an FPGA is doable, but to me seems much more complicated, though that might depend to a huge extent on the exact nature of the system you're dealing with.